chr2-145055594-A-C

Variant names:

• chr2-145055594-A-C
• rs955944
• ENST00000445791.5:n.308-15226A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000445791.5(TEX41):​n.308-15226A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,258 control chromosomes in the GnomAD database, including 210 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.018 (210 hom., cov: 32)
• Consequence: TEX41 ENST00000445791.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 3 publications found

Genes affected

TEX41 (HGNC:48667): (testis expressed 41)

LOC100505498 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445791.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	NR_033870.2		n.464-15226A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX41	ENST00000445791.5	TSL:1	n.308-15226A>C		intron	N/A
	TEX41	ENST00000451774.5	TSL:1	n.405-15226A>C		intron	N/A
	TEX41	ENST00000597173.6	TSL:1	n.433+32321A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2788 AN: 152140 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.00309

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0229

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0183 AC: 2787 AN: 152258 Hom.: 210 Cov.: 32 AF XY: 0.0204 AC XY: 1517 AN XY: 74442

African (AFR) AF: 0.00308 AC: 128 AN: 41570

American (AMR) AF: 0.135 AC: 2069 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.0892 AC: 462 AN: 5178

South Asian (SAS) AF: 0.00373 AC: 18 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000235 AC: 16 AN: 68014

Other (OTH) AF: 0.0232 AC: 49 AN: 2116

Alfa AF: 0.0291 Hom.: 177

Bravo AF: 0.0309

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.53
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs955944; hg19: chr2-145813161;